Ryota Takaki, UT-Austin

"Physics and Mathematical models for biological machines"

Abstract: Molecular motors are biological machines playing an essential role in cellular activity. In this talk, I discuss three projects for various biological motors that I have worked on during my degree. First, I introduce the possibly simplest model, which can recapitulate the transport of the cargos by kinesin-1. We derive the expression of the velocity distribution for kinesin-1. We propose that examination of the randomness parameter is valuable information to infer the chemo-mechanical kinetics involving the stepping mechanism for kinesin-1. The subsequent section analyzes the coordination in the chemo-mechanical cycle for kinesin-1, so-called gating, from non-equilibrium thermodynamics and information-theoretical perspective. The analysis illustrates that the stall load of kinesin-1 may be stemmed from the gating mechanism. In the last section, we turn the subject into the genome organization problem. We propose a simple theoretical model to explain the recently discovered loop extrusion process by novel molecular motors: Structural Maintenance of Chromosomes (SMC) proteins.